| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2051/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SWATH2stats 1.30.1 (landing page) Peter Blattmann
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the SWATH2stats package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SWATH2stats |
| Version: 1.30.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SWATH2stats_1.30.1.tar.gz |
| StartedAt: 2023-10-19 05:41:39 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 05:47:59 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 380.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SWATH2stats.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SWATH2stats_1.30.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SWATH2stats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.30.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘aLFQ’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SWATH2stats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) sample_annotation.Rd:29: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
load_mart 0.722 0.083 11.201
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
[ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plots.R:85:3'): variation plot vs total ──────────────────────
cv.val1.total == as.numeric(test1.total[, "cv"]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SWATH2stats.Rcheck/00check.log’
for details.
SWATH2stats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SWATH2stats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘SWATH2stats’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SWATH2stats)
SWATH2stats.Rcheck/tests/test-all.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
[ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plots.R:85:3'): variation plot vs total ──────────────────────
cv.val1.total == as.numeric(test1.total[, "cv"]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted
SWATH2stats.Rcheck/SWATH2stats-Ex.timings
| name | user | system | elapsed | |
| JPP_update | 0.135 | 0.007 | 0.261 | |
| add_genesymbol | 0.007 | 0.001 | 0.016 | |
| assess_decoy_rate | 0.126 | 0.005 | 0.238 | |
| assess_fdr_byrun | 0.209 | 0.010 | 0.388 | |
| assess_fdr_overall | 0.178 | 0.010 | 0.347 | |
| convert4MSstats | 0.622 | 0.015 | 1.135 | |
| convert4PECA | 0.194 | 0.005 | 0.356 | |
| convert4aLFQ | 0.645 | 0.016 | 1.178 | |
| convert4mapDIA | 0.413 | 0.012 | 0.760 | |
| convert4pythonscript | 0.174 | 0.006 | 0.321 | |
| convert_protein_ids | 0 | 0 | 0 | |
| count_analytes | 0.154 | 0.004 | 0.280 | |
| disaggregate | 0.255 | 0.009 | 0.478 | |
| filter_all_peptides | 0.172 | 0.006 | 0.321 | |
| filter_mscore | 0.193 | 0.006 | 0.362 | |
| filter_mscore_condition | 0.201 | 0.008 | 0.361 | |
| filter_mscore_fdr | 0.413 | 0.011 | 0.766 | |
| filter_mscore_freqobs | 0.196 | 0.004 | 0.356 | |
| filter_on_max_peptides | 0.185 | 0.004 | 0.335 | |
| filter_on_min_peptides | 0.182 | 0.004 | 0.343 | |
| filter_proteotypic_peptides | 0.175 | 0.005 | 0.307 | |
| import_data | 0.511 | 0.023 | 0.949 | |
| load_mart | 0.722 | 0.083 | 11.201 | |
| mscore4assayfdr | 0.348 | 0.009 | 0.636 | |
| mscore4pepfdr | 0.318 | 0.007 | 0.586 | |
| mscore4protfdr | 0.283 | 0.005 | 0.514 | |
| plot.fdr_cube | 0.210 | 0.009 | 0.402 | |
| plot.fdr_table | 0.176 | 0.006 | 0.324 | |
| plot_correlation_between_samples | 0.502 | 0.014 | 0.923 | |
| plot_variation | 0.492 | 0.019 | 0.919 | |
| plot_variation_vs_total | 0.461 | 0.015 | 0.871 | |
| reduce_OpenSWATH_output | 0.146 | 0.003 | 0.269 | |
| removeDecoyProteins | 0.152 | 0.005 | 0.278 | |
| sample_annotation | 0.208 | 0.007 | 0.397 | |
| transform_MSstats_OpenSWATH | 0.003 | 0.000 | 0.008 | |
| unifyProteinGroupLabels | 0.154 | 0.003 | 0.294 | |
| validate_columns | 0.001 | 0.001 | 0.002 | |
| write_matrix_peptides | 0.158 | 0.004 | 0.293 | |
| write_matrix_proteins | 0.176 | 0.005 | 0.329 | |